EuroSciPy logo


Cambridge, UK - 27-30 August 2014

Platform to Enable Shared Scientific Computing and Research Assets (PESSCARA)

Joshua Warner


PESSCARA is a cloud-based infrastructure designed to promote sharing of data, metadata, algorithms, and research in medical imaging. PESSCARA consists of a content management system that stores medical images and associated metadata/tags, with a development environment based on IPython. PESSCARA is characterized by a highly user-configurable workflow, exposing a unified interface that can store, manage, and retrieve imaging studies. Additionally, PESSCARA includes tools for data auditing, project management and administration, while it incorporates an open source content management system (TACTIC) and an image receiver tuned for DICOM (the standard medical image format).

To enable users to perform image processing on images within PESSCARA, we have implemented the IPython notebook environment and have coupled it to a Python library we have written called tiPY. tiPY enables simple input and output from the PESSCARA content management system. We chose IPython as a computational environment since it enables a single framework for rapid prototyping, algorithm development, inline documentation, and easy sharing of algorithms for collaboration in addition to interfacing with the large and growing universe of Python packages. This frees users from re-implementing many necessary, but mundane algorithms or additional analysis tools. IPython also allows easy access to the Linux shell for additional packages which may not yet have Python bindings. Finally, the scientific Python community offers a variety of tools to visualize results.

The components of PESSCARA are open source and can be implemented as a cloud solution. PESSCARA aims to provide the community with an environment suitable to deal with the requirements of medical image analysis adapted to the spirit of open and reproducible research.